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Old 04-11-2013, 11:57 AM   #41
jzx2002
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Location: new york

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Smile rRNA removal for Mycobacterium tuberculosis

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Originally Posted by epibio View Post
Please contact me using the link in my profile and I'd be happy to set you up with the evaluation program. Thank you.
Hi,
Do you know which kit is good to remove rRNA from MTB? We have problem by using RiboMinus kit (Cat# AM1905).
Thanks,
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Old 04-15-2013, 07:56 AM   #42
Olaf Blue
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Hello: the information we have with Ribo-Zero abd Mycobacterium tuberculosis is this:

"“RZ Bacteria - (Mycobacterium tuberculosis) Efficiently removes 23S, 16S and 5S rRNAs.”

Olaf
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Old 05-28-2013, 08:38 PM   #43
Ivy
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Default rRNA removal from yeast

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Originally Posted by epibio View Post
The H/M/R kit will give you >99% rRNA reduction from yeast, as long as you have high-quality (intact) RNA. If you're interested in beta-testing a yeast-specific kit, please send me a PM or contact me using the link on my profile page.
Hi. I'm trying to use the Ribo-zero rRNA removal kit(H/M/R kit) for rRNA depletion from yeast RNA. After sequencing, the rRNA levels left in my samples ranging from 15%-48%. Do you know what's the problem? Thanks.
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Old 05-29-2013, 06:36 AM   #44
Olaf Blue
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Hi Ivy,

The post you're is rather old, and as time has gone on we have found that (as many already say) that the Yeast rRNAs are simply too diverse to be able to be removed completely using the RZ H/M/R Kit. While some yeast species do work well with the H/M/R Kit, we have found that other less common strains are not as easily depleted.

There is a RZ Yeast kit under development, but you can also contact Epicentre's TS and submit your sequences for sequence checks against the capture probes in the kit.

By the way - which rRNA species are contributing the sequences in the 15-48% fraction?

Olaf
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Old 09-19-2013, 07:01 AM   #45
RickC7
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Default RNA-Seq and 5S

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Originally Posted by Olaf Blue View Post
Hello: the information we have with Ribo-Zero abd Mycobacterium tuberculosis is this:

"“RZ Bacteria - (Mycobacterium tuberculosis) Efficiently removes 23S, 16S and 5S rRNAs.”

Olaf
I am working on an RNA-Seq project and on epibio website under species compatibility it states for Mycobacterium tuberculosis "will not remove 5S". Looking at Agilent results I have to agree b/c we see a very distinct peak for the 5S region after using Ribo-Zero Magnetic Kit (Gram-Positive Bacteria) Cat. No. MRZGP126. 23S and 16S are gone. My concern is that a large portion of our reads from sequencing will be 5S region and we will reduce reads for the important stuff. Has anyone been successful at removing the 5S for such an experiment? Or do you just sequence more to achieve the desired depth?

I even see my library size range shifted. Usually I expect more reads >200bp, but in this case I have an increased distribution of fragments <200bp. I believe this to be the 5S region being fragmented even smaller and being carried through the rest of Library construction protocol. SoliD RNA-Seq standard protocol. I am very hesitant to proceed with sequencing. Does anyone have a similar experience?

Thanks.

Last edited by RickC7; 09-19-2013 at 07:06 AM.
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Old 09-19-2013, 07:38 AM   #46
Olaf Blue
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Generally RNA can be further enriched by size selection; I believe that 5s rRNA (about 110-120 nt) can be removed using a standard Qiagen RNEasy MiniKit as the kit will not retain any RNAs less than 200 nt. We almost never see any fragment size shift as the capture probes only interact/remove rRNA and do not affect the RNA quality in terms of insert length. What kit/method are you using for library prep?
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